Package: MAGeCKFlute

Version: 1.4.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MAGeCKFlute_1.4.3.tar.gz

StartedAt: 2019-10-16 04:13:03 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:22:32 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 569.2 seconds

RetCode: 0

Status:  OK

CheckDir: MAGeCKFlute.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MAGeCKFlute_1.4.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MAGeCKFlute.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MAGeCKFlute/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAGeCKFlute’ version ‘1.4.3’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MAGeCKFlute’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data      5.3Mb
    doc       1.2Mb
    extdata   9.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘MAGeCKFlute/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(paste(strwrap(disclaimer, 80), collapse = "\n"))

See section ‘Good practice’ in '?.onAttach'.

BatchRemove: no visible binding for global variable ‘PC1’
BatchRemove: no visible binding for global variable ‘PC2’
BatchRemove: no visible binding for global variable ‘shape’
CellCycleView: no visible binding for global variable ‘x’
CellCycleView: no visible binding for global variable ‘y’
DensityDiffView: no visible binding for global variable ‘Diff’
DensityDiffView: no visible binding for global variable ‘..density..’
DensityDiffView: no visible binding for global variable ‘r’
DensityView: no visible binding for global variable ‘value’
DensityView: no visible binding for global variable ‘variable’
EnrichedFilter: no visible binding for global variable ‘max_value’
EnrichedGeneView: no visible binding for global variable ‘Gene’
EnrichedGeneView: no visible binding for global variable ‘Term’
EnrichedGeneView: no visible binding for global variable ‘Size’
EnrichedGeneView: no visible binding for global variable ‘GeneScore’
EnrichedView: no visible binding for global variable ‘Description’
EnrichedView: no visible binding for global variable ‘size’
FluteMLE: no visible binding for global variable ‘Zuber_Essential’
KeggPathwayView: no visible global function definition for ‘keggConv’
KeggPathwayView: no visible binding for global variable ‘rn.list’
KeggPathwayView: no visible global function definition for
  ‘parseKGML2Graph2’
MapRatesView: no visible binding for global variable ‘count’
MapRatesView: no visible binding for global variable ‘category’
MapRatesView: no visible binding for global variable ‘pos’
MapRatesView: no visible binding for global variable ‘percent’
NormalizeBeta: no visible binding for global variable ‘Zuber_Essential’
RankView: no visible binding for global variable ‘Rank’
RankView: no visible binding for global variable ‘group’
RankView: no visible binding for global variable ‘Gene’
ScatterView: no visible binding for global variable ‘Control’
ScatterView: no visible binding for global variable ‘Treatment’
ScatterView: no visible binding for global variable ‘group’
Selector: no visible binding for global variable ‘GeneNum’
Selector: no visible binding for global variable ‘x’
Selector: no visible binding for global variable ‘y’
SquareView: no visible binding for global variable ‘x’
SquareView: no visible binding for global variable ‘y’
SquareView: no visible binding for global variable ‘group’
SquareView: no visible binding for global variable ‘Gene’
ViolinView: no visible binding for global variable ‘variable’
ViolinView: no visible binding for global variable ‘value’
VolcanoView: no visible binding for global variable ‘group’
VolcanoView: no visible binding for global variable ‘color’
sgRankView: no visible global function definition for ‘.’
sgRankView: no visible binding for global variable ‘LFC’
sgRankView: no visible binding for global variable ‘Gene’
sgRankView: no visible binding for global variable ‘x’
sgRankView: no visible binding for global variable ‘y’
sgRankView: no visible binding for global variable ‘value’
sgRankView: no visible binding for global variable ‘id’
sgRankView: no visible binding for global variable ‘yend’
Undefined global functions or variables:
  . ..density.. Control Description Diff Gene GeneNum GeneScore LFC PC1
  PC2 Rank Size Term Treatment Zuber_Essential category color count
  group id keggConv max_value parseKGML2Graph2 percent pos r rn.list
  shape size value variable x y yend
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
enrich.ORT       35.540  0.633  36.183
MAView           33.537  0.218  33.783
EnrichAnalyzer   28.083  1.437  29.464
EnrichedFilter   22.789  1.296  22.965
EnrichedGeneView 22.418  1.248  22.609
arrangePathview  22.430  1.070  25.448
enrich.HGT       19.342  0.492  19.829
TransGeneID      14.059  0.187  14.246
getOrg           12.872  0.169  13.079
gsGetter          9.989  0.331  10.466
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/MAGeCKFlute.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MAGeCKFlute
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MAGeCKFlute’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MAGeCKFlute)

name	user	system	elapsed
BatchRemove	1.863	0.070	1.935
CellCycleView	0.686	0.085	0.771
CutoffCalling	0.004	0.000	0.004
DensityDiffView	1.564	0.126	1.692
DensityView	1.067	0.078	1.147
EnrichAB	0.065	0.015	0.080
EnrichAnalyzer	28.083	1.437	29.464
EnrichSquare	0.434	0.340	0.150
EnrichedFilter	22.789	1.296	22.965
EnrichedGeneView	22.418	1.248	22.609
EnrichedView	0.000	0.000	0.001
FluteMLE	0.002	0.001	0.003
FluteRRA	0.004	0.003	0.007
HeatmapView	0.376	0.028	0.404
IdentBarView	0.198	0.003	0.200
KeggPathwayView	0.030	0.006	0.035
MAView	33.537	0.218	33.783
MapRatesView	0.574	0.010	0.585
NormalizeBeta	0.302	0.025	0.327
RankView	2.320	0.082	2.403
ReadBeta	0.035	0.012	0.047
ReadRRA	0.601	0.010	0.610
ReadsgRRA	0.195	0.043	0.238
ScatterView	0.962	0.086	1.048
Selector	0.331	0.004	0.336
SquareView	1.742	0.100	1.842
TransGeneID	14.059	0.187	14.246
ViolinView	2.851	0.257	3.111
VolcanoView	3.842	0.164	4.008
arrangePathview	22.430	1.070	25.448
countsummary	0.009	0.004	0.011
enrich.GSE	0.015	0.001	0.015
enrich.HGT	19.342	0.492	19.829
enrich.ORT	35.540	0.633	36.183
getOrg	12.872	0.169	13.079
gsGetter	9.989	0.331	10.466
mle.gene_summary	0.041	0.010	0.052
normalize.loess	0.515	0.045	0.560
rra.gene_summary	0.037	0.005	0.042
rra.sgrna_summary	0.544	0.045	0.589
sgRankView	1.994	1.086	1.685